Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Payen M, Nicolis I, Robin M, Michonneau D, Delannoye J, Mayeur C, Kapel N, Berçot B, Butel MJ, Le Goff J, Socié G, Rousseau C
Journal
Blood advances
Year
2020
Acute graft-versus-host disease (aGVHD) is the main complication of hematopoietic stem cell transplantation (HSCT). Changes in gut microbiota composition have been associated with subsequent aGVHD, and reconstitution of healthy microbiota is currently being explored as a therapeutic approach. However, the specific actors in the intestinal ecosystem involved in the pathologic process at the time of aGVHD onset are not yet fully known. We prospectively collected stool samples from patients who underwent allogeneic HSCT. Patients sampled at aGVHD onset were compared with non-GVHD patients. To identify phylogenetic and functional signatures of the disease process, we determined fecal short-chain fatty acid (SFCA) profiles and used high-throughput DNA sequencing and real-time quantitative polymerase chain reaction to assess the microbiota composition. Microbiota alterations were highly specific of gastrointestinal (GI) aGVHD severity. Bacterial biomass and α-diversity were lower in severe aGVHD. We identified several bacterial signatures associated with severe aGVHD at disease onset; a negative correlation was observed with anaerobic bacteria of the Lachnospiraceae, especially the Blautia genus, and Ruminococcaceae families. In parallel, in severe aGVHD patients, we showed a dramatic decrease in the levels of the main SFCAs: acetate (75.8%), propionate (95.8%), and butyrate (94.6%). Mild aGVHD patients were characterized by conserved levels of propionate and Blautia propionate producers. Butyrate was significantly decreased in all GI aGVHD stages, representing a potential diagnostic marker of the disease. Specific microbiota and metabolic alterations were thus associated with aGVHD severity and may be useful for diagnostic and pathophysiologic purposes.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Location of subjects
- France
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Graft versus host disease disease, graft-versus-host,disease, graft-VS-host,disease, homologous wasting,disease, runt,diseases, graft-versus-host,diseases, graft-VS-host,graft versus host disease,graft VS host disease,graft VS. host disease,graft-versus-host disease,graft-versus-host disease, resistance to,graft-versus-host disease, susceptibility to,graft-versus-host diseases,graft-versus-host-disease,graft-VS-host disease,graft-VS-host diseases,GVH,GVHD,GVHDS,homologous wasting disease,runt disease,Graft versus host disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe acute graft-versus-host-disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2B
Description: Differential relative abundance between controls and severe acute graft-versus- host disease patients.
Abundance in Group 1: increased abundance in Severe acute graft-versus-host-disease
| NCBI | Quality Control | Links |
|---|---|---|
| Lactococcus | ||
| Lautropia | ||
| Stenotrophomonas | ||
| Xanthomonadaceae | ||
| Xanthomonadales | ||
| Prevotella sp. |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2B
Description: Differential relative abundance between controls and severe acute graft-versus- host disease patients.
Abundance in Group 1: decreased abundance in Severe acute graft-versus-host-disease
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3)
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2C
Description: Differential relative abundance between controls and severe acute graft-versus-host disease patients.
Abundance in Group 1: increased abundance in Severe acute graft-versus-host-disease
| NCBI | Quality Control | Links |
|---|---|---|
| Stenotrophomonas | ||
| Prevotella |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2C
Description: Differential relative abundance between controls and severe acute graft-versus- host disease patients.
Abundance in Group 1: decreased abundance in Severe acute graft-versus-host-disease
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Thomasclavelia ramosa | ||
| Faecalibacterium sp. UBA1819 | ||
| Flavonifractor | ||
| Lachnoclostridium | ||
| Lachnospiraceae | ||
| Sellimonas | ||
| Oscillospiraceae |
Revision editor(s): Claregrieve1, WikiWorks
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